RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354253.markdup.sorted.bam gff file = gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf counting algorithm = uniquely-mapped-reads protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 >>>>>>> Reads alignment reads aligned (left/right) = 30,549,913 / 30,537,413 read pairs aligned = 30,535,104 total alignments = 65,375,283 secondary alignments = 4,287,957 non-unique alignments = 6,973,828 aligned to genes = 51,978,879 ambiguous alignments = 203,655 no feature assigned = 5,863,617 not aligned = 1,130,136 >>>>>>> Reads genomic origin exonic = 51,978,879 (89.86%) intronic = 3,931,028 (6.8%) intergenic = 1,932,589 (3.34%) overlapping exon = 1,689,528 (2.92%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.22 5'-3' bias = 1.97 >>>>>>> Junction analysis reads at junctions = 17,452,726 ACCT : 5.42% AGGT : 4.65% ATCT : 3.6% AGGA : 3.52% TCCT : 3.48% GCCT : 3.37% AGCT : 2.61% CCCT : 2.41% AGGC : 2.35% AGAT : 2.27% TTCT : 2.18%